My turn on the commentary on the list!

Comments in Bold

Opening:

Consider the more radical re-edits to the entire movie (RotJ: Fan-O-Matic) I agree the movie needs a lot of help.
Change the opening crawl to something more dramatic than "Luke Skywalker has returned to his home planet of Tatooine in an attempt to rescue his friend Han Solo from the clutches of the vile gangster Jabba The Hutt" See number 1
Add evidence of construction vehicles working on the Death Star, maybe even as just hints of movement around the incomplete side. I like this idea.
Replace the shot of the Star Destroyer going overhead with a shot of the shuttle coming from the Executor. Vader coming from a regular Star Destroyer doesn't make sense. Yes, its like the first movie, but this movie is enough like the first one as it is.

Tatooine:

Remove Boba Fett from the film. I could not agree more.
Change Jawa eyes to match ANH. Noticed the Jawas, never noticed the difference.
"Cantina"-ize Jabba's speech and expressions. Ady knows how to make it subtle.
"Cantina"-ize other aliens in the Palace. Sure, if any of them stand still long enough.
Make Bib Fortuna's tentacles move occasionally. Pointless, but probably easy enough.
Remove Greedo's dialog from the background noice in Jabba's Palace. One of those things where once its been pointed out, its all you can hear.
Remove 3PO's line of "Look, it's Captain Solo and he's still frozen in Carbonite!" I'm not against this line.
Cut down on Salacious Crumb's laughter. I don't mind the little bugger.
Cut/shorten the Droid Torture scene. Never understood why / how droid torture worked. Trim it definately.
Remove Jedi Rocks. Very yes.
Remove Fett flirting with the dancer. No Fett.
Restore Lapti Nek. If you must. I'm not about any dance numbers in the movie.
Fix the flipped shots of Fett. No Fett.
Change Boushh's dialog to be a more "realistic" language. With no lips to match, we have free reign.
Mix up Jabba's minion's reaction to Boushh's thermal detenator so Fett isn't the only one who pulls out his gun. Not sure how this would be possible.
Cut Lando pulling his mask down after he hits his head on the low ceiling. Nothing wrong with that, but...
Remove Lando hitting his head on the low ceiling. ...that needs help.
Remove the belch from the creature outside Jabba's Palace. Eh, this could stay or go.
Enhance the carbonite thawing process. Always up for more shiny.
Add Han's restraints when he is unfrozen. Yay, continuity!
Remove Han's scene with Chewie in the dungeons. Not sure why we would do that.
Remove Luke using Force Choke on the guards. Force Choke really doesn't fit in with the Jedi code.
Add Mara Jade (from the EU) to Jabba's Palace. If we get rid of the Boba Fett fanwank, why put another in?
Cut the Rancor Keeper's mourning. Nothing wrong with keeping this in. It's pointless, but nothing wrong with it.
Remove SE Bantha herd. I like the herd.
Restore pre-SE Sarlacc. I like the beak.
Add more menancing sounds to the SE Sarlacc. I'd like the beak better if it didn't sound like a "dying seagull."
Fix jump cut as R2's panel comes open and the lightsaber pops up. All jump cuts need fixed.
Add the knob to the top of the emitter to the saber that comes out of R2. Sure, continuity is great.
Shorten the amount of time Luke has his hand in the air waiting for his lightsaber. Reducing the time Luke stands with his hand in the air in this movie would be great.
"Restore" Luke's lightsaber to the preproduction blue. Fun to see, pointless to do.
Make it so Luke's lightsaber leaves slash marks on Jabba's crew. Yes, please.
Remove/replace the scream as Fett spirals out of control. No Fett.
Make it so Han deliberately hits or shoots Fett using shots from later in the movie. No Fett.
Make it so Luke beheads Fett. No Fett.
Make it so Luke deflects a bolt at Fett which sets off his backpack. No Fett.
Fix Fett's jetpack as they come out at the wrong angle currently. No Fett.
Have Fett shoot at the Sarlacc as he falls into it. No Fett.
Add a shot of Fett crawling/flying out of the Sarlacc. No Fett.
Fix it so Luke actually kicks the guard while Fett flies out of control in the background. This use of "Force Kick" has always bothered me / cracked me up.
Restore Han's "Trust me" line. Could go either way. Maybe we could use both lines?
Make it so Luke doesn't have his hand straight up in the air to get shot. See number 30.
Remove Luke's hand damage from before he gets shot. Continuity please.
Attempt to restore the deleted Sandstorm scene and remove the ship-to-ship conversation. Impossible to do.

Dagobah:

"Cantina"-ize Yoda. Yes, subtle.
Do something about Yoda's obvious rubber hand during his death scene. Yoda always had rubber hands...
Tweak/cut Yoda's disappearance. Tweak yes, or make Obi Wan the only Jedi who disappears.
Recolor the blue Force Ghosts to prevent confusion with blue holograms. No, ghosts don't have scan lines.
No Luke/Leia relation. Interesting if one could make it work with the rest of the movie. Does seem rather tacked on.

Rebel Fleet:

Recut Rebel Briefing. Sure, here and there.
Shorten/cut the huggy Luke and Co. reunion ("I'm with you too" and on). Eh, maybe.
Different Shuttle Class for Tydyrium. Definately yes. "Parts and Technical" use the same class of ship as the EMPEROR?!
Replace/enhance matte painting of Rebel docking bay. Replace the matte.

Forest Moon of Endor:

Add Endor so that the Forest Moon is actually a moon of something. Yes, a la Yavin.
Change Ewoks to Wookiees. Impossible.
Complete removal of Ewoks. Come on, with some tweaking, they could be great.
"Cantina"-ize the Ewoks. Yes, very much.
Add 3PO's line "I believe they are called... Ewoks" from the Radio Drama. I love this idea.
Stabilize the speeder bikes during the chase. Never noticed, but sure.
Adjust the scene so it looks like the Scout pushes Luke off of his speeder bike. Luke bailing out on is pretty lame, but his landing shows that he was prepared for it.
Do something with Leia remembering her mother, her real mother. Yes, either cut this (I expected Lucas to in 2004) or fix RotS.
Change Vader's line of "Obi-wan once thought as you do" to "Your mother once thought as you do". I'd have to hear it first.
Cut Teebo's Speeder Bike Adventure. I could go either way.
Add more Imperial laser fire as the Ewoks attack. I'm always up for more lasers, no matter the color.
Add AT-AT to ground battle. Impossible.
Cut Chewie's Tarzan yell. Yes, even though I saw Tarzan AFTER Jedi and thought he was making fun of Chewie.
Enhance AT-ST explosion that is crushed between the two logs. Better explosions are always welcome.
Enhance AT-ST explosion that is shot by Chewie's AT-ST. See number 14.
Remove Harrison Ford's reflection from safety glass as he runs from the bunker. Yes, bothered me forever. They fixed the reflection in Raiders without calling it a "Special Edition", but couldn't do it here?
The shield generator explosion is huge and looks like it would probably wipe out everyone in the area. It is a little big, but totally awesome!

Death Star Attack:

Rebel fighters crashing into the DS shield. Very yes!
More fighters overall (B-wings and A-wings especially). Sure, in the less crowed scenes add some B-Wings blowing the crap out of an SD.
Fix garbage spots in "one of the battle shots" where ships were not added. Garbage is always bad.
Just before Lando says "Yes, I said closer", some of the background ships don't tilt with the rest of the shot. All mistakes should be fixed.
Remove green matte boxes around ships. Matte boxes are inexcusable.
Remove/replace some of the copy/paste capital ships. I understand only having one or two models, but they could at least take pictures from different angles.
Add more laser fire as the capital ships should be pounding on one another (a la the RotS opening). Yes, especially the shots of the fighters flying between them.
Add shots of Rebel capital ships attacking the surface of the DS (storyboard) That'd be cool.
Better end to the Executor. Never really thought it was bad, but some of the suggestions I read are much more awesome.
Add shots of the gunner stations on the DS (from ANH). Eh, not needed. This battle is more about piloting through the interior and less about dodging laser fire.
Redub the Rebel pilot line: "Copy, Gold Leader". As long as its me. ;-)
Kill Lando, blow up the Falcon. Justify Han's feeling like he's "never going to see her again." I'd really love this, if it works.
Remove ring from DS explosion. Whole new explosion with chunks, please!

Death Star Interior - Luke/Vader Duel:

Replace/enhance cardboard troopers during the Emperor's arrival. Call the 501st, have them stand at attention. Ta-da, replacement troops!
Replace the Emperor's advisers with Nemoidians. Pointless.
Fix the Emperor's "slugs". Still don't understand them or notice them, but I want them gone!
Move the exterior battle closer to the Throne Room window as it should be (a la the RotS opening). Closer, but not too close. And remember, ALL of the fighters left fly into the Death Star when the shields come down.
Remove/soften the more obvious lightsaber blade shadows. I am a firm believer that light doesn't cast a shadow.
Fix large black matte that covers half the screen when Vader is kicked down the stars. Never saw it, but fix it!
Fix Vader's blade coming out the wrong end of his saber as he throws it to cut the catwalk. Sometimes I pause to laugh at that, so fixing it would deprive me of pointing it out and laughing.
Remove Luke's lightsaber from Vader's hand while Luke is hiding. Yes, unfortunately we can't restore WHY he had it in the first place.
Edit Vader's dialog to hiding Luke to remove some cheesy lines. I like the lines.
Add Luke pulling his lightsaber out of Vader's hand after he is done hiding. Unless we can explain why Vader had it, he doesn't need it.
Add Sith eyes while Luke is beating Vader. Eh, no.
Cut some of Luke's angry hits on Vader while he's down. I'd say add more!
Add more Sith Lightning. Not sure how you can add more, but sure.
Tighten up Vader's hesitation to save Luke from the Emperor. Maybe a second or two...
Add Qui Gon voiceover to Vader's hesitation to imply that Qui Gon passes his secrets of Jedi Ghosthood to Anakin. How about no?
Add flashbacks to Vader's hesitation of Padme, his mother, Qui Gon, etc. Eh, no.
Fix saber on/off issues. I'm sure Ady will figure out when the sabers are supposed to be on or off.
Restore Sebastian Shaw's eyebrows to the unmasking scene. I'm not too hot on that.
Fix the transition from Sebastian Shaw's face to the bald cap he wears. Sure, why not?

Ending:

Fix Luke's lazy eye as he looks at the funeral pyre. Never noticed.
Add Leia viewing the funeral pyre. She doesn't care.
Remove SE celebrations. Yes, the rest of the galaxy wouldn't know, unless they were watching it live on pay-per-view.
Restore pre-2004 buildings to the background of the Coruscant celebration. Its a city planet, why do the building we see have to be next to the only two buildings we ever see there?
Remove the "Weesa free!" line from the Naboo celebration. Unless Gungans are toned down in TMPR, keep it.
Restore Yub Nub. No. Just no. That is a terrible way to end the saga. End that movie, yes; end that trilogy, maybe; end the whole 6 episode plus saga, no.
Restore Sebastian Shaw as Anakin's Force Ghost. Yes.
Attempt to morph Shaw and Christensen into the Anakin Force Ghost. That would be weird, I think, since Shaw looks happy and Christensen looks creepy.
Add other Jedi from the prequels appearing next to Obi-wan, Yoda, and Anakin. A bit cheesy.